Date of introduction and epidemiologic patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Mogadishu, Somalia: estimates from transmission modelling of satellite-based excess mortality data in 2020.

Mihaly Koltai,Cmmid Covid-19 Working Group ,Farah Bashiir,Nicholas G Davies,Abdirisak Dalmar,Ahmed Aweis,Mohamed Ahmed,Chris Williams,Terri Freemantle,Abdihamid Warsame,Chris Reeve,Stefan Flasche,Francesco Checchi,Mark Jit

doi:10.12688/wellcomeopenres.17247.1

Abstract

Background: In countries with weak surveillance systems, confirmed coronavirus disease 2019 (COVID-19) deaths are likely to underestimate the pandemic's death toll. Many countries also have incomplete vital registration systems, hampering excess mortality estimation. Here, we fitted a dynamic transmission model to satellite imagery data of cemeteries in Mogadishu, Somalia during 2020 to estimate the date of introduction and other epidemiologic parameters of the early spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in this low-income, crisis-affected setting. Methods: We performed Markov chain Monte Carlo (MCMC) fitting with an age-structured compartmental COVID-19 model to provide median estimates and credible intervals for the date of introduction, the basic reproduction number ( R 0 ) and the effect of non-pharmaceutical interventions (NPIs) up to August 2020. Results: Under the assumption that excess deaths in Mogadishu March-August 2020 were attributable to SARS-CoV-2 infections, we arrived at median estimates of November-December 2019 for the date of introduction and low R 0 estimates (1.4-1.7) reflecting the slow and early rise and long plateau of excess deaths. The date of introduction, the amount of external seeding, the infection fatality rate (IFR) and the effectiveness of NPIs are correlated parameters and not separately identifiable in a narrow range from deaths data. Nevertheless, to obtain introduction dates no earlier than November 2019 a higher population-wide IFR (≥0.7%) had to be assumed than obtained by applying age-specific IFRs from high-income countries to Somalia's age structure. Conclusions: Model fitting of excess mortality data across a range of plausible values of the IFR and the amount of external seeding suggests an early SARS-CoV-2 introduction event may have occurred in Somalia in November-December 2019. Transmissibility in the first epidemic wave was estimated to be lower than in European settings. Alternatively, there was another, unidentified source of sustained excess mortality in Mogadishu from March to August 2020.

Highlights

By September 2021, more than 4.7 million people were confirmed to have died from the coronavirus disease 2019 (COVID-19) pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
While the first COVID-19 cases in sub-Saharan African countries were identified in late February[12] (16th of March in Somalia), there is considerable uncertainty about the true date of introduction, often estimated to be in January 2020 for Western Europe[13], or as early as December 2019 according to retrospective polymerase chain reaction (PCR) on routine patient samples[14]
Fit quality as expressed by DIC values are similar for population-wide infection fatality rate (IFR) between 0.36% and 1.6% (Figure 3), but much poorer when using the high-income country-specific base assumption of 0.15%

Summary

Introduction

By September 2021, more than 4.7 million people were confirmed to have died from the coronavirus disease 2019 (COVID-19) pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While the first COVID-19 cases in sub-Saharan African countries were identified in late February[12] (16th of March in Somalia), there is considerable uncertainty about the true date of introduction, often estimated to be in January 2020 for Western Europe[13], or as early as December 2019 according to retrospective PCR on routine patient samples[14] For these reasons, alternative data sources such as obituaries[9] and satellite imagery[15] of cemeteries have been leveraged to estimate the true scale of COVID-19 mortality and its early spread in low- and middle-income countries in Africa and elsewhere. The date of introduction, the amount of external seeding, the infection fatality rate (IFR) and the effectiveness of NPIs are correlated parameters and not separately

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Conclusion